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Journal articles on the topic 'Ubiquitin'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 August 2024

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1

Kama, Rachel, Galina Gabriely, Vydehi Kanneganti, and Jeffrey E. Gerst. "Cdc48 and ubiquilins confer selective anterograde protein sorting and entry into the multivesicular body in yeast." Molecular Biology of the Cell 29, no. 8 (April 15, 2018): 948–63. http://dx.doi.org/10.1091/mbc.e17-11-0652.

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Cdc48/p97 is known primarily for the retrotranslocation of misfolded proteins in endoplasmic reticulum (ER)-associated protein degradation (ERAD). Here we uncover a novel function for both Cdc48 and the conserved ubiquitin-associated/ubiquitin-like ubiquitin receptor (ubiquilin) proteins in yeast (e.g., Ddi1, Dsk2, and Rad23), which deliver ubiquitinated proteins to the proteasome for degradation. We show that Cdc48, its core adaptors Npl4 and Ufd1, and the ubiquilins confer the constitutive anterograde delivery of carboxypeptidase S (Cps1), a membranal hydrolase, to the multivesicular body (MVB) and vacuolar lumen. Cdc48 and Ddi1 act downstream of Rsp5-dependent Cps1 ubiquitination to facilitate the disassembly of insoluble Cps1 oligomers and upstream of ESCRT-0 to facilitate the entry of soluble protein into the MVB. Consequentially, detergent-insoluble Cps1 accumulates in cells bearing mutations in CDC48, DDI1, and all three ubiquilins (ddi1Δ, dsk2Δ, rad23Δ). Thus, Cdc48 and the ubiquilins have ERAD- and proteasome-independent functions in the anterograde delivery of specific proteins to the yeast vacuole for proteolytic activation. As Cdc48/p97 and the ubiquilins are major linkage groups associated with the onset of human neurodegenerative disease (e.g., amytrophic lateral sclerosis, Alzheimer’s, and Paget’s disease of the bone), there may be a connection between their involvement in anterograde protein sorting and disease pathogenesis.

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2

Lee, Dong Yun, and Eric J. Brown. "Ubiquilins in the crosstalk among proteolytic pathways." Biological Chemistry 393, no. 6 (June 1, 2012): 441–47. http://dx.doi.org/10.1515/hsz-2012-0120.

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Abstract Protein degradation occurs through several distinct proteolytic pathways for membrane and cytosolic proteins. There is evidence that these processes are linked and that crosstalk among these major protein degradation pathways occurs. Ubiquilins, a family of ubiquitin-binding proteins, are involved in all protein degradation pathways. This minireview provides an overview of ubiquilin function in protein degradation and contrasts it with sequestosome-1 (p62), a protein that also has been implicated in multiple proteolytic pathways.

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3

Jantrapirom, Salinee, Luca Lo Piccolo, Dumnoensun Pruksakorn, Saranyapin Potikanond, and Wutigri Nimlamool. "Ubiquilin Networking in Cancers." Cancers 12, no. 6 (June 15, 2020): 1586. http://dx.doi.org/10.3390/cancers12061586.

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Ubiquilins or UBQLNs, members of the ubiquitin-like and ubiquitin-associated domain (UBL-UBA) protein family, serve as adaptors to coordinate the degradation of specific substrates via both proteasome and autophagy pathways. The UBQLN substrates reveal great diversity and impact a wide range of cellular functions. For decades, researchers have been attempting to uncover a puzzle and understand the role of UBQLNs in human cancers, particularly in the modulation of oncogene’s stability and nucleotide excision repair. In this review, we summarize the UBQLNs’ genetic variants that are associated with the most common cancers and also discuss their reliability as a prognostic marker. Moreover, we provide an overview of the UBQLNs networks that are relevant to cancers in different ways, including cell cycle, apoptosis, epithelial-mesenchymal transition, DNA repairs and miRNAs. Finally, we include a future prospective on novel ubiquilin-based cancer therapies.

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4

Hurtley, Stella M. "One Ubiquitin, Two Ubiquitin, Three Ubiquitin, Four." Science's STKE 2007, no. 369 (January 16, 2007): tw26. http://dx.doi.org/10.1126/stke.3692007tw26.

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The role of protein ubiquitination is well known in promoting regulated protein degradation. Mukhopadhyay and Riezman review what is known about the contribution of protein ubiquitination in other cellular pathways, including intracellular signaling, endocytosis, and protein sorting.D. Mukhopadhyay, H. Riezman, Proteasome-independent functions of ubiquitin in endocytosis and signaling. Science315, 201-205 (2007). [Abstract][Full Text]

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5

Hill, Spencer, Joseph S. Harrison, Steven M. Lewis, Brian Kuhlman, and Gary Kleiger. "Mechanism of Lysine 48 Selectivity during Polyubiquitin Chain Formation by the Ube2R1/2 Ubiquitin-Conjugating Enzyme." Molecular and Cellular Biology 36, no. 11 (April 4, 2016): 1720–32. http://dx.doi.org/10.1128/mcb.00097-16.

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Lysine selectivity is of critical importance during polyubiquitin chain formation because the identity of the lysine controls the biological outcome. Ubiquitins are covalently linked in polyubiquitin chains through one of seven lysine residues on its surface and the C terminus of adjacent protomers. Lys 48-linked polyubiquitin chains signal for protein degradation; however, the structural basis for Lys 48 selectivity remains largely unknown. The ubiquitin-conjugating enzyme Ube2R1/2 has exquisite specificity for Lys 48, and computational docking of Ube2R1/2 and ubiquitin predicts that Lys 48 is guided to the active site through a key electrostatic interaction between Arg 54 on ubiquitin and Asp 143 on Ube2R1/2. The validity of this interaction was confirmed through biochemical experiments. Since structural examples involving Arg 54 in protein-ubiquitin complexes are exceedingly rare, these results provide additional insight into how ubiquitin-protein complexes can be stabilized. We discuss how these findings relate to how other ubiquitin-conjugating enzymes direct the lysine specificity of polyubiquitin chains.

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6

Ford, Diana L., and Mervyn J. Monteiro. "Dimerization of ubiquilin is dependent upon the central region of the protein: evidence that the monomer, but not the dimer, is involved in binding presenilins." Biochemical Journal 399, no. 3 (October 13, 2006): 397–404. http://dx.doi.org/10.1042/bj20060441.

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Ubiquilin proteins have been shown to interact with a wide variety of other cellular proteins, often regulating the stability and degradation of the interacting protein. Ubiquilin contains a UBL (ubiquitin-like) domain at the N-terminus and a UBA (ubiquitin-associated) domain at the C-terminus, separated by a central region containing Sti1-like repeats. Little is known about regulation of the interaction of ubiquilin with other proteins. In the present study, we show that ubiquilin is capable of forming dimers, and that dimerization requires the central region of ubiquilin, but not its UBL or the UBA domains. Furthermore, we provide evidence suggesting that monomeric ubiquilin is likely to be the active form that is involved in binding presenilin proteins. Our results provide new insight into the regulatory mechanism underlying the interaction of ubiquilin with presenilins.

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7

Seok Ko, Han, Takashi Uehara, Kazuhiro Tsuruma, and Yasuyuki Nomura. "Ubiquilin interacts with ubiquitylated proteins and proteasome through its ubiquitin-associated and ubiquitin-like domains." FEBS Letters 566, no. 1-3 (April 28, 2004): 110–14. http://dx.doi.org/10.1016/j.febslet.2004.04.031.

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8

Chatrin, Chatrin, Mads Gabrielsen, Lori Buetow, Mark A. Nakasone, Syed F. Ahmed, David Sumpton, Gary J. Sibbet, Brian O. Smith, and Danny T. Huang. "Structural insights into ADP-ribosylation of ubiquitin by Deltex family E3 ubiquitin ligases." Science Advances 6, no. 38 (September 2020): eabc0418. http://dx.doi.org/10.1126/sciadv.abc0418.

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Cellular cross-talk between ubiquitination and other posttranslational modifications contributes to the regulation of numerous processes. One example is ADP-ribosylation of the carboxyl terminus of ubiquitin by the E3 DTX3L/ADP-ribosyltransferase PARP9 heterodimer, but the mechanism remains elusive. Here, we show that independently of PARP9, the conserved carboxyl-terminal RING and DTC (Deltex carboxyl-terminal) domains of DTX3L and other human Deltex proteins (DTX1 to DTX4) catalyze ADP-ribosylation of ubiquitin’s Gly76. Structural studies reveal a hitherto unknown function of the DTC domain in binding NAD+. Deltex RING domain recruits E2 thioesterified with ubiquitin and juxtaposes it with NAD+ bound to the DTC domain to facilitate ADP-ribosylation of ubiquitin. This ubiquitin modification prevents its activation but is reversed by the linkage nonspecific deubiquitinases. Our study provides mechanistic insights into ADP-ribosylation of ubiquitin by Deltex E3s and will enable future studies directed at understanding the increasingly complex network of ubiquitin cross-talk.

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9

Morgan, Rachel E., Vijay Chudasama, Paul Moody, Mark E. B. Smith, and Stephen Caddick. "A novel synthetic chemistry approach to linkage-specific ubiquitin conjugation." Organic & Biomolecular Chemistry 13, no. 14 (2015): 4165–68. http://dx.doi.org/10.1039/c5ob00130g.

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10

Ikeda, Hiromi, and Tom K. Kerppola. "Lysosomal Localization of Ubiquitinated Jun Requires Multiple Determinants in a Lysine-27–Linked Polyubiquitin Conjugate." Molecular Biology of the Cell 19, no. 11 (November 2008): 4588–601. http://dx.doi.org/10.1091/mbc.e08-05-0496.

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Ubiquitination regulates many cellular functions, including protein localization and degradation. Each function is specified by unique determinants in the conjugate. Ubiquitinated Jun is localized to lysosomes for degradation. Here, we characterized determinants of Jun ubiquitination and lysosomal localization by using ubiquitin-mediated fluorescence complementation (UbFC) in living cells and analysis of the stoichiometry of ubiquitin linked to Jun extracted from cells. The δ region of Jun and isoleucine-44 in ubiquitin were required for lysosomal localization of the conjugate. Ubiquitin containing only lysine-27, but no other single-lysine ubiquitin, mediated Jun ubiquitination, albeit at lower stoichiometry than wild-type ubiquitin. These conjugates were predominantly nuclear, but coexpression of lysine-27 and lysine-less ubiquitins enhanced the mean stoichiometry of Jun ubiquitination and lysosomal localization of the conjugate. Hepatocyte growth factor-regulated tyrosine kinase substrate (HRS) and tumor susceptibility gene 101 (TSG101) colocalized with ubiquitinated Jun. Knockdown of HRS or TSG101 inhibited lysosomal localization of ubiquitinated Jun and reduced Jun turnover. Ubiquitination of other Fos and Jun family proteins had distinct effects on their localization. Our results indicate that Jun is polyubiquitinated by E3 ligases that produce lysine-27–linked chains. Lysosomal localization of the conjugate requires determinants in Jun and in ubiquitin that are recognized in part by TSG101 and HRS, facilitating selective translocation and degradation of ubiquitinated Jun.

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11

Liu, Ling, J. Roger H. Frappier, Karen d'Ailly, Burr G. Atkinson, Daniel S. Maillet, and David B. Walden. "Characterization, chromosomal mapping, and expression of different ubiquitin fusion protein genes in tissues from control and heat-shocked maize seedlings." Biochemistry and Cell Biology 74, no. 1 (January 1, 1996): 9–19. http://dx.doi.org/10.1139/o96-002.

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Organisms possess at least two multigene families of ubiquitins: the polyubiquitins, with few to several repeat units, which encode a ubiquitin monomer, and the ubiquitin fusion (or extension) protein genes, which encode a single ubiquitin monomer and a specific protein. This report provides details about two ubiquitin fusion protein genes in maize referred to as MubG7 (uwo 1) and MubG10 (uwo 2). Each has one nearly identical ubiquitin coding unit fused without an intervening nucleotide to an unrelated, 237-nucleotide sequence that encodes for a 79 amino acid protein. The derived amino acid sequences of the two fusion proteins show that they differ by five amino acids (substitution by either a serine or threonine). MubG7 maps to chromosome 8L162 and MubG10 maps to chromosome 1L131. Analyses of the role(s) of these genes in response to heat shock (1 h at 42.5 °C) reveal that the level of these fusion protein mRNAs in the radicles or plumules from 2-day-old seedlings does not change; however, heat shock does cause a marked reduction in the accumulation of these same gene-specific mRNAs in the radicles and plumules of 5-day-old seedlings. These data confirm the suggestion from our earlier work that there is precise modulation, in a gene-specific manner, of the response to developmental as well as environmental signals.Key words: ubiquitin, ubiquitin extension (or fusion) protein, maize, heat shock, heat shock proteins, gene expression, chromosome map.

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12

FRIED, V. A., and H. T. SMITH. "UBIQUITIN." Alzheimer Disease & Associated Disorders 2, no. 3 (1988): 188. http://dx.doi.org/10.1097/00002093-198802030-00037.

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13

Hipkiss, A. R. "Ubiquitin." FEBS Letters 268, no. 2 (August 1, 1990): 431–32. http://dx.doi.org/10.1016/0014-5793(90)81300-d.

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14

Board, Philip G. "Ubiquitin." Trends in Genetics 5 (1989): 161. http://dx.doi.org/10.1016/0168-9525(89)90061-9.

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15

Chuang, Kun-Han, Fengshan Liang, Ryan Higgins, and Yanchang Wang. "Ubiquilin/Dsk2 promotes inclusion body formation and vacuole (lysosome)-mediated disposal of mutated huntingtin." Molecular Biology of the Cell 27, no. 13 (July 2016): 2025–36. http://dx.doi.org/10.1091/mbc.e16-01-0026.

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Ubiquilin proteins contain a ubiquitin-like domain (UBL) and ubiquitin-associated domain(s) that interact with the proteasome and ubiquitinated substrates, respectively. Previous work established the link between ubiquilin mutations and neurodegenerative diseases, but the function of ubiquilin proteins remains elusive. Here we used a misfolded huntingtin exon I containing a 103-polyglutamine expansion (Htt103QP) as a model substrate for the functional study of ubiquilin proteins. We found that yeast ubiquilin mutant ( dsk2Δ) is sensitive to Htt103QP overexpression and has a defect in the formation of Htt103QP inclusion bodies. Our evidence further suggests that the UBL domain of Dsk2 is critical for inclusion body formation. Of interest, Dsk2 is dispensable for Htt103QP degradation when Htt103QP is induced for a short time before noticeable inclusion body formation. However, when the inclusion body forms after a long Htt103QP induction, Dsk2 is required for efficient Htt103QP clearance, as well as for autophagy-dependent delivery of Htt103QP into vacuoles (lysosomes). Therefore our data indicate that Dsk2 facilitates vacuole-mediated clearance of misfolded proteins by promoting inclusion body formation. Of importance, the defect of inclusion body formation in dsk2 mutants can be rescued by human ubiquilin 1 or 2, suggesting functional conservation of ubiquilin proteins.

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16

Pruneda, Jonathan N., Kate E. Stoll, Laura J. Bolton, Peter S. Brzovic, and Rachel E. Klevit. "Ubiquitin in Motion: Structural Studies of the Ubiquitin-Conjugating Enzyme∼Ubiquitin Conjugate." Biochemistry 50, no. 10 (March 15, 2011): 1624–33. http://dx.doi.org/10.1021/bi101913m.

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17

Vertegaal, Alfred C. O. "Uncovering Ubiquitin and Ubiquitin-like Signaling Networks." Chemical Reviews 111, no. 12 (December 14, 2011): 7923–40. http://dx.doi.org/10.1021/cr200187e.

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18

Jahngen-Hodge, Jessica, Deanna Cyr, Eric Laxman, and Allen Taylor. "Ubiquitin and ubiquitin conjugates in human lens." Experimental Eye Research 55, no. 6 (December 1992): 897–902. http://dx.doi.org/10.1016/0014-4835(92)90016-l.

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19

Park, Hee Jin, Hyeong Cheol Park, Sang Yeol Lee, Hans J. Bohnert, and Dae-Jin Yun. "Ubiquitin and Ubiquitin-like Modifiers in Plants." Journal of Plant Biology 54, no. 5 (July 23, 2011): 275–85. http://dx.doi.org/10.1007/s12374-011-9168-5.

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20

Saifee, Nabiha Huq, and Ning Zheng. "A Ubiquitin-like Protein Unleashes Ubiquitin Ligases." Cell 135, no. 2 (October 2008): 209–11. http://dx.doi.org/10.1016/j.cell.2008.09.049.

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21

Yip, Matthew C. J., Nicholas O. Bodnar, and Tom A. Rapoport. "Ddi1 is a ubiquitin-dependent protease." Proceedings of the National Academy of Sciences 117, no. 14 (March 19, 2020): 7776–81. http://dx.doi.org/10.1073/pnas.1902298117.

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TheSaccharomyces cerevisiaeprotein Ddi1 and its homologs in higher eukaryotes have been proposed to serve as shuttling factors that deliver ubiquitinated substrates to the proteasome. Although Ddi1 contains both ubiquitin-interacting UBA and proteasome-interacting UBL domains, the UBL domain is atypical, as it binds ubiquitin. Furthermore, unlike other shuttling factors, Ddi1 and its homologs contain a conserved helical domain (helical domain of Ddi1, HDD) and a retroviral-like protease (RVP) domain. The RVP domain is probably responsible for cleavage of the precursor of the transcription factor Nrf1 in higher eukaryotes, which results in the up-regulation of proteasomal subunit genes. However, enzymatic activity of the RVP domain has not yet been demonstrated, and the function of Ddi1 remains poorly understood. Here, we show that Ddi1 is a ubiquitin-dependent protease, which cleaves substrate proteins only when they are tagged with long ubiquitin chains (longer than about eight ubiquitins). The RVP domain is inactive in isolation, in contrast to its retroviral counterpart. Proteolytic activity of Ddi1 requires the HDD domain and is stimulated by the UBL domain, which mediates high-affinity interaction with the polyubiquitin chain. Compromising the activity of Ddi1 in yeast cells results in the accumulation of polyubiquitinated proteins. Aside from the proteasome, Ddi1 is the only known endoprotease that acts on polyubiquitinated substrates. Ddi1 and its homologs likely cleave polyubiquitinated substrates under conditions where proteasome function is compromised.

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22

Liu, Weigang, Xun Tang, Xuehong Qi, Xue Fu, Shantwana Ghimire, Rui Ma, Shigui Li, Ning Zhang, and Huaijun Si. "The Ubiquitin Conjugating Enzyme: An Important Ubiquitin Transfer Platform in Ubiquitin-Proteasome System." International Journal of Molecular Sciences 21, no. 8 (April 21, 2020): 2894. http://dx.doi.org/10.3390/ijms21082894.

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Owing to a sessile lifestyle in nature, plants are routinely faced with diverse hostile environments such as various abiotic and biotic stresses, which lead to accumulation of free radicals in cells, cell damage, protein denaturation, etc., causing adverse effects to cells. During the evolution process, plants formed defense systems composed of numerous complex gene regulatory networks and signal transduction pathways to regulate and maintain the cell homeostasis. Among them, ubiquitin-proteasome pathway (UPP) is the most versatile cellular signal system as well as a powerful mechanism for regulating many aspects of the cell physiology because it removes most of the abnormal and short-lived peptides and proteins. In this system, the ubiquitin-conjugating enzyme (E2) plays a critical role in transporting ubiquitin from the ubiquitin-activating enzyme (E1) to the ubiquitin-ligase enzyme (E3) and substrate. Nevertheless, the comprehensive study regarding the role of E2 enzymes in plants remains unexplored. In this review, the ubiquitination process and the regulatory role that E2 enzymes play in plants are primarily discussed, with the focus particularly put on E2′s regulation of biological functions of the cell.

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23

Pan, Jia-Xiu, Sharla R. Short, Stephen A. Goff, and J. Fred Dice. "Ubiquitin pools, ubiquitin mRNA levels, and ubiquitin-mediated proteolysis in aging human fibroblasts." Experimental Gerontology 28, no. 1 (January 1993): 39–49. http://dx.doi.org/10.1016/0531-5565(93)90018-9.

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24

Nakamura, Nobuhiro. "Ubiquitin System." International Journal of Molecular Sciences 19, no. 4 (April 4, 2018): 1080. http://dx.doi.org/10.3390/ijms19041080.

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25

Cesari, Francesca. "Catching ubiquitin." Nature Reviews Molecular Cell Biology 9, no. 7 (June 4, 2008): 498–99. http://dx.doi.org/10.1038/nrm2431.

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26

Chenette, Emily J. "Free ubiquitin!" Nature Reviews Molecular Cell Biology 10, no. 10 (September 3, 2009): 653. http://dx.doi.org/10.1038/nrm2765.

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27

LeBrasseur, Nicole. "Ubiquitin stripping." Journal of Cell Biology 166, no. 4 (August 16, 2004): 443. http://dx.doi.org/10.1083/jcb1664iti4.

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28

Swatek, Kirby N., and David Komander. "Ubiquitin modifications." Cell Research 26, no. 4 (March 25, 2016): 399–422. http://dx.doi.org/10.1038/cr.2016.39.

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29

Burge, Rebecca J., Jeremy C. Mottram, and Anthony J. Wilkinson. "Ubiquitin and ubiquitin-like conjugation systems in trypanosomatids." Current Opinion in Microbiology 70 (December 2022): 102202. http://dx.doi.org/10.1016/j.mib.2022.102202.

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30

Welchman, Rebecca L., Colin Gordon, and R. John Mayer. "Ubiquitin and ubiquitin-like proteins as multifunctional signals." Nature Reviews Molecular Cell Biology 6, no. 8 (August 2005): 599–609. http://dx.doi.org/10.1038/nrm1700.

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31

Majetschak, Matthias, Norbert Ponelies, and Thomas Hirsch. "Targeting the monocytic ubiquitin system with extracellular ubiquitin." Immunology & Cell Biology 84, no. 1 (February 2006): 59–65. http://dx.doi.org/10.1111/j.1440-1711.2005.01399.x.

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32

Shang, Fu, Gejing Deng, Qing Liu, Weimin Guo, Arthur L. Haas, Bernat Crosas, Daniel Finley, and Allen Taylor. "Lys6-modified Ubiquitin Inhibits Ubiquitin-dependent Protein Degradation." Journal of Biological Chemistry 280, no. 21 (March 24, 2005): 20365–74. http://dx.doi.org/10.1074/jbc.m414356200.

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33

Ernst, Andreas. "Engineering ubiquitin to modulate the ubiquitin proteosome system." Cell Cycle 12, no. 11 (June 2013): 1651–52. http://dx.doi.org/10.4161/cc.24985.

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34

Hoeller, Daniela, Christina-Maria Hecker, and Ivan Dikic. "Ubiquitin and ubiquitin-like proteins in cancer pathogenesis." Nature Reviews Cancer 6, no. 10 (October 2006): 776–88. http://dx.doi.org/10.1038/nrc1994.

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35

Mattern, Michael, James Sutherland, Karteek Kadimisetty, Rosa Barrio, and Manuel S. Rodriguez. "Using Ubiquitin Binders to Decipher the Ubiquitin Code." Trends in Biochemical Sciences 44, no. 7 (July 2019): 599–615. http://dx.doi.org/10.1016/j.tibs.2019.01.011.

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36

Pelisch, F., G. Risso, and A. Srebrow. "RNA metabolism and ubiquitin/ubiquitin-like modifications collide." Briefings in Functional Genomics 12, no. 1 (November 22, 2012): 66–71. http://dx.doi.org/10.1093/bfgp/els053.

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37

Matsuda, Noriyuki. "Phospho-ubiquitin: upending the PINK–Parkin–ubiquitin cascade." Journal of Biochemistry 159, no. 4 (February 2, 2016): 379–85. http://dx.doi.org/10.1093/jb/mvv125.

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38

Hartmann-Petersen, Rasmus, Klavs B. Hendil, and Colin Gordon. "Ubiquitin binding proteins protect ubiquitin conjugates from disassembly." FEBS Letters 535, no. 1-3 (December 27, 2002): 77–81. http://dx.doi.org/10.1016/s0014-5793(02)03874-7.

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39

Denison, Carilee, Donald S. Kirkpatrick, and Steven P. Gygi. "Proteomic insights into ubiquitin and ubiquitin-like proteins." Current Opinion in Chemical Biology 9, no. 1 (February 2005): 69–75. http://dx.doi.org/10.1016/j.cbpa.2004.10.010.

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40

Herrmann, Joerg, Lilach O. Lerman, and Amir Lerman. "Ubiquitin and Ubiquitin-Like Proteins in Protein Regulation." Circulation Research 100, no. 9 (May 11, 2007): 1276–91. http://dx.doi.org/10.1161/01.res.0000264500.11888.f0.

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41

Di Fiore, Pier Paolo, Simona Polo, and Kay Hofmann. "When ubiquitin meets ubiquitin receptors: a signalling connection." Nature Reviews Molecular Cell Biology 4, no. 6 (June 2003): 491–97. http://dx.doi.org/10.1038/nrm1124.

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42

Srikumar, Tharan, Stanley M. Jeram, Henry Lam, and Brian Raught. "A ubiquitin and ubiquitin-like protein spectral library." PROTEOMICS 10, no. 2 (January 2010): 337–42. http://dx.doi.org/10.1002/pmic.200900627.

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43

Majetschak, Matthias, Markus Laub, Helmut E. Meyer, and Herbert P. Jennissen. "The ubiquityl-calmodulin synthetase system from rabbit reticulocytes : isolation of the ubiquitin-binding first component, a ubiquitin-activating enzyme." European Journal of Biochemistry 255, no. 2 (July 15, 1998): 482–91. http://dx.doi.org/10.1046/j.1432-1327.1998.2550482.x.

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44

Saha, Anjanabha, Steven Lewis, Gary Kleiger, Brian Kuhlman, and Raymond J. Deshaies. "Essential Role for Ubiquitin-Ubiquitin-Conjugating Enzyme Interaction in Ubiquitin Discharge from Cdc34 to Substrate." Molecular Cell 42, no. 1 (April 2011): 75–83. http://dx.doi.org/10.1016/j.molcel.2011.03.016.

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45

Gao, Yi, Wei Mo, Li Zhong, Huimin Jia, Yiren Xu, Ji Zhang, Xiaohui Xu, et al. "Downregulation of Ubiquitin Inhibits the Aggressive Phenotypes of Esophageal Squamous Cell Carcinoma." Technology in Cancer Research & Treatment 19 (January 1, 2020): 153303382097328. http://dx.doi.org/10.1177/1533033820973282.

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Purpose: Esophageal cancer is one of the most common malignancies worldwide. Ubiquitin-dependent degradation of regulatory proteins reportedly plays a central role in diverse cellular processes. This study investigated the expression levels of ubiquitin in esophageal squamous cell carcinoma tissues and the functions of ubiquitin in the context of esophageal squamous cell carcinoma progression. Methods: The expression of ubiquitin in esophageal squamous cell carcinoma and normal esophageal samples was determined via immunohistochemistry. Serum ubiquitin levels were determined by enzyme-linked immunosorbent assay. The association between serum ubiquitin level and clinicopathological factors was analyzed. Real-time PCR analysis was employed to measure the mRNA levels of the ubiquitin coding genes ubiquitin B and ubiquitin C. Proliferation assays, colony formation assays, and Transwell-based assays were used to determine the influence of ubiquitin on cell growth and cell invasion. Proteomic analysis was performed to identify the proteins associated with ubiquitin. Results: Ubiquitin expression in esophageal squamous cell carcinoma tissues was markedly higher than that in normal and tumor adjacent tissues. The levels of ubiquitin in esophageal squamous cell carcinoma serum samples were significantly higher than those in healthy controls. Serum ubiquitin levels were correlated with tumor stage and lymph node metastasis. To silence the expression of ubiquitin, we knocked down the ubiquitin coding genes ubiquitin B and ubiquitin C in TE-1 and Eca-109 cells. Silencing ubiquitin resulted in the suppression of cell growth, chemoresistance, colony formation and cell migration in esophageal squamous cell carcinoma cells. Proteomic analysis in esophageal squamous cell carcinoma cells showed that knockdown of ubiquitin coding genes deregulated the expression of 159 proteins (92 were upregulated and 67 were downregulated) involved in multiple pathways. These proteins included ferritin light chain, ferritin heavy chain, cellular retinoic acid-binding protein 2, and DNA replication factor 1. Conclusion: Ubiquitin expression is upregulated in esophageal squamous cell carcinoma tissues and serum samples. Serum ubiquitin levels were correlated with tumor stage and lymph node metastasis. Downregulation of ubiquitin suppresses the aggressive phenotypes of esophageal squamous cell carcinoma cells by complex mechanisms; ubiquitin may represent a novel target for the treatment of esophageal squamous cell carcinoma.

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Schäfer, Antje, Monika Kuhn, and Hermann Schindelin. "Structure of the ubiquitin-activating enzyme loaded with two ubiquitin molecules." Acta Crystallographica Section D Biological Crystallography 70, no. 5 (April 30, 2014): 1311–20. http://dx.doi.org/10.1107/s1399004714002910.

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Abstract:

The activation of ubiquitin by the ubiquitin-activating enzyme Uba1 (E1) constitutes the first step in the covalent modification of target proteins with ubiquitin. This activation is a three-step process in which ubiquitin is adenylated at its C-terminal glycine, followed by the covalent attachment of ubiquitin to a catalytic cysteine residue of Uba1 and the subsequent adenylation of a second ubiquitin. Here, a ubiquitin E1 structure loaded with two ubiquitin molecules is presented for the first time. While one ubiquitin is bound in its adenylated form to the active adenylation domain of E1, the second ubiquitin represents the status after transfer and is covalently linked to the active-site cysteine. The covalently linked ubiquitin enables binding of the E2 enzyme without further modification of the ternary Uba1–ubiquitin2arrangement. This doubly loaded E1 structure constitutes a missing link in the structural analysis of the ubiquitin-transfer cascade.

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Watson, Ian R., and Meredith S. Irwin. "Ubiquitin and Ubiquitin-Like Modifications of the p53 Family." Neoplasia 8, no. 8 (August 2006): 655–66. http://dx.doi.org/10.1593/neo.06439.

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KITAHARA, Ryo. "Evolutionary-Conserved Intermediates among Ubiquitin and Ubiquitin-Like Proteins." Seibutsu Butsuri 49, no. 1 (2009): 020–22. http://dx.doi.org/10.2142/biophys.49.020.

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Nicholson, Benjamin, Craig A. Leach, Seth J. Goldenberg, Dana M. Francis, Matthew P. Kodrasov, Xufan Tian, John Shanks, et al. "Characterization of ubiquitin and ubiquitin-like-protein isopeptidase activities." Protein Science 17, no. 6 (June 2008): 1035–43. http://dx.doi.org/10.1110/ps.083450408.

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Kerscher, Oliver, Rachael Felberbaum, and Mark Hochstrasser. "Modification of Proteins by Ubiquitin and Ubiquitin-Like Proteins." Annual Review of Cell and Developmental Biology 22, no. 1 (November 2006): 159–80. http://dx.doi.org/10.1146/annurev.cellbio.22.010605.093503.

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